The specified Python version just refers to the runtime environment for
Jedi. Use the Python 2 version if you’re running vim (or whatever editor you
use) under Python 2. Otherwise, use the Python 3 version. But whatever version
you choose, both are able to complete both Python 2 and 3 code.

If you use an editor plugin like jedi-vim, you can simply include Jedi as a
git submodule of the plugin directory. Vim plugin managers like Vundle or
Pathogen make it very easy to keep submodules up to date.